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Apo crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 BuviA.00139.a.B1 PS01581 at 26.1 mg/mL against MCSG 1 screen condition G5, 2 M ammonium sulfate, 0.1 M BisTris pH 6.5, with 20% ethylene glycol as cryo-protectant, crystal tracking ID 236782g5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.83 67.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.42 α = 90 b = 116.42 β = 90 c = 89.97 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ VariMax 2012-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 50 99.3 0.073 21.94 10.3 44492 44198 -3 34.916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 97.6 0.417 4.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VHL 2.05 44.02 44196 2234 99.33 0.2028 0.2012 0.2075 0.2338 0.2378 RANDOM 33.514
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.22 0.22 0.22 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 19.725 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 5.761 r_angle_refined_deg 1.46 r_angle_other_deg 0.81 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 19.725 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 5.761 r_angle_refined_deg 1.46 r_angle_other_deg 0.81 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3052 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 55
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction